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phyloTop provides tools for calculating and viewing topological properties of phylogenetic trees.
To install the development version from github:
library(devtools)
install_github("michellekendall/phyloTop")The stable version can be installed from CRAN using:
install.packages("phyloTop")Then, to load the package, use:
library("phyloTop")
## Loading required package: apeThe key functions available in phyloTop are:
avgLadder: find the average ladder
size in a tree
cherries: find the number of
cherries in a tree
colless.phylo: find the Colless
imbalance number of a tree
getDepths: find the depth of each
node in a tree
ILnumber: find the number of nodes
with exactly one tip child
ladderSizes: find the size of any
“ladders” in a tree (consecutive nodes, each with exactly one tip
child)
maxHeight: find the maximum height
(equivalently, depth) of nodes in a tree
nConfig: find the sizes of all
configurations (equivalently, clades) in a tree
nodeDepth: find the depth of a
given node in a tree
nodeDepthFrac: find the fraction of
nodes in a tree at a given depth
nodeImb: find the imbalance of a
given node in a tree
nodeImbFrac: find the fraction of
nodes in a tree with an imbalance of a given threshold or more
phyloTop: find a range of tree
statistics for a list of trees (faster than calling each function
individually)
pitchforks: find the number of
pitchforks (clades of size three) in a tree
sackin.phylo: find the Sackin index
of a tree
splitTop: find the split topology
of a tree - the size of clades at a given depth
stairs: find the “staircase-ness”
measures, as defined by Norstrom et al. 2012
treeImb: find the tree imbalance -
the imbalance at each node
widths: find the number of nodes at
each depth in a tree
configShow: plot a tree,
highlighting the configurations of a given size
ladderShow: plot a tree,
highlighting the “ladders”
subtreeShow: plot a tree,
highlighting the subtree(s) descending from the given node(s)
makeEpiRecord: simulate an
epidemiological record of infectors, infectees, infection times and
recovery times
getLabGenealogy: create a genealogy
from an epidemiological record
Apply tree statistic functions to a list of 10 random trees, each with 50 tips:
set.seed(123)
phyloTop(rmtree(10,50))
## avgLadder cherries colless.phylo ILnumber maxHeight pitchforks sackin.phylo
## 1 0.000 19 82 12 9 9 312
## 2 2.167 16 120 18 9 7 330
## 3 2.500 19 192 12 12 6 394
## 4 2.333 16 139 18 11 9 345
## 5 2.000 18 150 14 10 8 358
## 6 2.333 17 105 16 11 10 321
## 7 2.333 19 112 12 10 5 330
## 8 2.333 15 229 20 13 9 421
## 9 3.000 17 121 16 11 7 331
## 10 3.000 16 181 18 12 7 377
## stairs1 stairs2
## 1 0.5510 0.7257
## 2 0.5306 0.6752
## 3 0.5102 0.6907
## 4 0.6327 0.6487
## 5 0.5714 0.6880
## 6 0.6122 0.6649
## 7 0.5714 0.6696
## 8 0.6735 0.5760
## 9 0.6122 0.6487
## 10 0.6122 0.6237Plot a random tree with 20 tips, highlighting the the clade(s) descending from nodes 25 and 33:
subtreeShow(rtree(20),nodeList=c(25,33), mainCol="navy", subtreeCol="cyan", nodeLabelCol="cyan", edge.width=2)
Contributions are welcome via pull requests.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Questions, feature requests and bugs can be reported using the package’s issue system.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.